AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -irpoE_ctra_opreg_300.orf -g0.413 -x5 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.413
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	sucC	69	Succinyl-CoA Synthetase, Beta
#2	htrA	138	DO Serine Protease

Motif number 1

CTTCAATCAACTTTGATTACTCA         	1	2	0	CTTTATTCTC	    0.970921	-68
TCCTCCTTATCTTTTATTATTCTTTTTACTTC	1	30	0	CTTTATTTTC	    0.990869	-40
  AAATAACCCTTTAATTTTTCCTCCTTATCT	1	50	0	CTTTATTTTC	    0.990869	-20
AAGGGGACTACTCTGATGATTCTCCAATCTAA	2	15	0	CTCTATGTTC	    0.994647	-124
AGCATACAAAATCTAATGATGCAAATCAAGGG	2	42	0	ATCTATGTGC	     0.97727	-97
ATCATTAGATTTTGTATGCTGCATATCTGCTT	2	54	1	TTTGATGTGC	    0.965683	-85
GCATATCTGCTTGTTATGGTGCATAAAATGAA	2	74	1	TTGTATGTGC	    0.976302	-65
          **** *** ***

Masking position 6
Map Score:   9.11361

Number of sites scoring better than the average of aligned sites = 94
Number in coding regions = 94
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 2

TATCTTTTATTATTCTTTTTACTTCAATCA	1	25	0	TATTCTTTTT	    0.915894	-45
CTTTAATTTTTCCTCCTTATCTTTTATTAT	1	42	0	TCCTCCTTAT	    0.950668	-28
ATCAGAGTAGTCCCCTTGATTTGCATCATT	2	30	1	TCCCCTTGAT	    0.990107	-109
ATGCTGCATATCTGCTTGTTATGGTGCATA	2	69	1	TCTGCTTGTT	    0.975761	-70
GCCCCTTTTTTTTTCATTTTATGCACCATA	2	88	0	TTTTCATTTT	    0.825704	-51
GGGCGTCTAGGCCCCTTTTTTTTTCATTTT	2	98	0	GCCCCTTTTT	    0.970764	-41
        CTTTTCCTTGATAAGCGATCTG	2	127	0	TTTCCTTGAT	    0.965521	-12
          **********

Masking position 7
Map Score:   4.50967

Number of sites scoring better than the average of aligned sites = 617
Number in coding regions = 615
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 3

CAAAGTTGATTGAAGTAAAAAGAATAATAA	1	19	1	TGAAGTAAAA	    0.918093	-51
CAAAATCTAATGATGCAAATCAAGGGGACT	2	38	0	TGATGCAAAT	    0.987715	-101
AGATTTTGTATGCTGCATATCTGCTTGTTA	2	60	1	TGCTGCATAT	     0.98607	-79
CTGCTTGTTATGGTGCATAAAATGAAAAAA	2	80	1	TGGTGCATAA	    0.945132	-59
          **********

Masking position 7
Map Score:   2.48857

Number of sites scoring better than the average of aligned sites = 51
Number in coding regions = 51
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 4

ATGCAAATCAAGGGGACTACTCTGATGATT	2	26	0	AGGGGACTAC	    0.997589	-113
TGAAAAAAAAAGGGGCCTAGACGCCCAGAT	2	102	1	AGGGGCCTAG	    0.996581	-37
          **********

Masking position 8
Map Score:   0.355481

Number of sites scoring better than the average of aligned sites = 2
Number in coding regions = 2
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 5

          **********

No masking
Map Score:   -2.59896e-14

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 6

          **********

No masking
Map Score:   -2.59896e-14

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 7

          **********

No masking
Map Score:   -2.59896e-14

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0